recipe bioconductor-biodbhmdb

biodbHmdb, a library for connecting to the HMDB Database






The biodbHmdb library is an extension of the biodb framework package that provides access to the HMDB Metabolites database. It allows to download the whole HMDB Metabolites database locally, access entries and search for entries by name or description. A future version of this package will also include a search by mass and mass spectra annotation.

package bioconductor-biodbhmdb

(downloads) docker_bioconductor-biodbhmdb



depends bioconductor-biodb:


depends bioconductor-biodb:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-r6:

depends r-rcpp:

depends r-testthat:

depends r-zip:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-biodbhmdb

and update with::

   mamba update bioconductor-biodbhmdb

To create a new environment, run:

mamba create --name myenvname bioconductor-biodbhmdb

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-biodbhmdb/tags`_ for valid values for ``<tag>``)

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